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Post-docs Itay Yanai, left, and Steve Vokes. Click on the posters to download the full versions (1.6MB each).

“Revealing the Functional Components of Gene Expression by Comparative Transcriptomics” won the Genome Research poster competition at Cold Spring Harbor’s “Systems Biology: Global Regulation of Gene Expression” meeting, held March 29-April 1st, 2007.  Itay Yanai, a post-doc in the Craig Hunter lab, created a poster about exploring the degree of differences in gene expression between two organisms (C. elegans and C. briggsae) that are morphologically near-identical but genetically more different than human is to mouse. “To assay for gene expression we designed two whole-genome microarrays, each specific to one of the organisms, and measured levels of gene expression across the first quarter of embryogenesis. We found a tremendous amount of differences – over 40% of orthologs (pairs of corresponding genes between species) have a divergent expression pattern. In particular we found that different categories of gene genes evolve at different rates, where functionally crucial genes have very similar expression profiles between the organisms and genes not expected to be relevant to embryogenesis tend to be more different, said Yanai”. 

MCB took 2nd place in the contest, as well.  Steve Vokes is a post-doc in the Andrew McMahon lab.  His poster, titled “Whole Genome Identification of the Gli3 Cis-Regulatory In Mammalian Digit Specification” also received high honors.  Vokes’ poster pertained specifically to the identification of the transcriptional circuitry directly downstream of Sonic hedgehog in the developing mouse limb bud.

“Systems biology is a holistic approach to understanding how all components of a biological process interact with each other. Applying this approach is a very interesting way to revisit classic paradigms in embryonic development such as digit specification. In conjunction with conventional developmental methods, these experiments are giving new insights into the general principles of mammalian gene regulation during development”, said Vokes.

Both posters are on display on the wall outside the MCB Imaging Center, 2nd floor, 16 Divinity Ave.

Yanai AbstractA gene’s pattern of expression is generally assumed to correlate to its
function, yet recent work has called this fundamental assumption into
question. If a fraction of gene expression corresponds to non-functional
regulation, how can it be distinguished from the functional component? From
an evolutionary perspective, if a gene’s expression profile in a specific
context is under selection it is expected to be conserved throughout evolution, whereas free of selection, it may change and adopt different
expression profiles. Thus, comparisons of expression profiles in related
species can identify which expression profiles are under selection and
likely to be functional. This approach is similar to comparing homologous
gene sequences, where conservation is generally interpreted as separating
the functional from the non-functional domains. Nematodes constitute a
fitting test-bed for this approach since the early embryonic development of
C. elegans is indistinguishable from that of C. briggsae, yet their genomes
are roughly as distant as the human and mouse genomes. We conducted an
embryonic time-course in both organisms, using a custom whole-genome
microarray for each. Comparing the temporal profiles of orthologous genes we
found that only ~60% are correlated between the two organsims. Genes whose profile evolved are significantly less likely to produce lethality when disrupted than genes with conserved profiles, suggesting that their embryonic expression is not under selection. These results indicate that expression comparisons over multiple species and developmental stages will identify the functional component of expression. [download poster]

Vokes AbstractThe Sonic hedgehog (Shh) signaling pathway plays critical roles at multiple steps during embryonic development. Reflecting this key role, many congenital birth defects in humans are caused by mis-regulation of this pathway. Digit formation and identity in the developing vertebrate embryo is mediated by a secreted morphogen gradient of Shh. Embryos lacking Shh activity fail to form digits (except for the thumb), while embryos expressing additional, ectopic Shh within the limb bud have extra digits (polydactyly). Shh signaling is mediated transcriptionally by three Gli transcription factors (Gli1-3), which act as context-dependent transcriptional activators or repressors. Despite years of study, the distinct targets that effect Gli signaling are poorly understood. This study defines, for the first time, the complete set of in vivo binding sites for a transcription factor in the context of a distinct developmental process in a vertebrate embryo.

We performed whole-genome chromatin immunoprecipitation with E11.5 mouse limb buds using tiling arrays that contained the entire mouse genome tiled at a 25bp resolution. This identified approximately 2,000 high quality Gli3 binding sites (including enhancers in all genes previously implicated in Shh signaling in the limb bud). Because Gli3 can act as either a transcriptional activator or repressor, and because many ChIP binding sites do not correspond to actively regulated loci, we determined gene expression profiles in the limb bud using a total of 5 genetic backgrounds that gave a spectrum of phenotypes from a complete loss of Shh activity to a maximal-gain-of-function. This information was used to define classes of genes that were differentially regulated by Shh signaling in different backgrounds. We then intersected these classes with the ChIP binding data to map these putative enhancers to various classes of Gli targets that are activated or repressed. These results, a subset of which we are validating in transgenic embryos, have important implications for understanding the organization of enhancer modules in the mammalian genome. [download poster]

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